We are implementing VisualCron as a replacement for some homemade transfer script, but we are missing an important feature in the SFT/ftp and file transfer jobs.
After completion we need to move the file to a new folder to a depending on if the transfer is successfull or have failed.

Or do we have to revert back to homemade scripts to do this?

Add another task after the ftp task. Use the File, Copy files task. You can optionally delete the source file there, so it becomes a move file.